1
|
Lai JZ, Lin CY, Chen SJ, Cheng YM, Abe M, Lin TC, Chien FC. Temporal-Focusing Multiphoton Excitation Single-Molecule Localization Microscopy Using Spontaneously Blinking Fluorophores. Angew Chem Int Ed Engl 2024:e202404942. [PMID: 38641901 DOI: 10.1002/anie.202404942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Single-molecule localization microscopy (SMLM) based on temporal-focusing multiphoton excitation (TFMPE) and single-wavelength excitation is used to visualize the three-dimensional (3D) distribution of spontaneously blinking fluorophore-labeled subcellular structures in a thick specimen with a nanoscale-level spatial resolution. To eliminate the photobleaching effect of unlocalized molecules in out-of-focus regions for improving the utilization rate of the photon budget in 3D SMLM imaging, SMLM with single-wavelength TFMPE achieves wide-field and axially confined two-photon excitation (TPE) of spontaneously blinking fluorophores. TPE spectral measurement of blinking fluorophores is then conducted through TFMPE imaging at a tunable excitation wavelength, yielding the optimal TPE wavelength for increasing the number of detected photons from a single blinking event during SMLM. Subsequently, the TPE fluorescence of blinking fluorophores is recorded to obtain a two-dimensional TFMPE-SMLM image of the microtubules in cancer cells with a localization precision of 18±6 nm and an overall imaging resolution of approximately 51 nm, which is estimated based on the contribution of Nyquist resolution and localization precision. Combined with astigmatic imaging, the system is capable of 3D TFMPE-SMLM imaging of brain tissue section of a 5XFAD transgenic mouse with the pathological features of Alzheimer's disease, revealing the distribution of neurotoxic amyloid-beta peptide deposits.
Collapse
Affiliation(s)
- Jian-Zong Lai
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Chun-Yu Lin
- College of Photonics, National Yang Ming Chiao Tung University, No.301, Sec.2, Gaofa 3rd Rd., Guiren Dist., Tainan City, 71150, Taiwan
| | - Shean-Jen Chen
- College of Photonics, National Yang Ming Chiao Tung University, No.301, Sec.2, Gaofa 3rd Rd., Guiren Dist., Tainan City, 71150, Taiwan
| | - Yu-Min Cheng
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Manabu Abe
- Department of Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8526, Japan
| | - Tzu-Chau Lin
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Fan-Ching Chien
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| |
Collapse
|
2
|
Starling T, Carlon-Andres I, Iliopoulou M, Kraemer B, Loidolt-Krueger M, Williamson DJ, Padilla-Parra S. Multicolor lifetime imaging and its application to HIV-1 uptake. Nat Commun 2023; 14:4994. [PMID: 37591879 PMCID: PMC10435470 DOI: 10.1038/s41467-023-40731-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
Simultaneous imaging of nine fluorescent proteins is demonstrated in a single acquisition using fluorescence lifetime imaging microscopy combined with pulsed interleaved excitation of three laser lines. Multicolor imaging employing genetically encodable fluorescent proteins permits spatio-temporal live cell imaging of multiple cues. Here, we show that multicolor lifetime imaging allows visualization of quadruple labelled human immunodeficiency viruses on host cells that in turn are also labelled with genetically encodable fluorescent proteins. This strategy permits to simultaneously visualize different sub-cellular organelles (mitochondria, cytoskeleton, and nucleus) during the process of virus entry with the potential of imaging up to nine different spectral channels in living cells.
Collapse
Affiliation(s)
- Tobias Starling
- Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London, UK
| | - Irene Carlon-Andres
- Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London, UK
| | - Maro Iliopoulou
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Randall Division of Cell and Molecular Biophysics and Department of Physics, King's College London, London, UK
| | - Benedikt Kraemer
- PicoQuant GmbH, Rudower Chaussee 29 (IGZ), 12489, Berlin, Germany
| | | | - David J Williamson
- Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London, UK
| | - Sergi Padilla-Parra
- Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London, UK.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK.
| |
Collapse
|
3
|
Nguyen TD, Chen YI, Chen LH, Yeh HC. Recent Advances in Single-Molecule Tracking and Imaging Techniques. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:253-284. [PMID: 37314878 DOI: 10.1146/annurev-anchem-091922-073057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Since the early 1990s, single-molecule detection in solution at room temperature has enabled direct observation of single biomolecules at work in real time and under physiological conditions, providing insights into complex biological systems that the traditional ensemble methods cannot offer. In particular, recent advances in single-molecule tracking techniques allow researchers to follow individual biomolecules in their native environments for a timescale of seconds to minutes, revealing not only the distinct pathways these biomolecules take for downstream signaling but also their roles in supporting life. In this review, we discuss various single-molecule tracking and imaging techniques developed to date, with an emphasis on advanced three-dimensional (3D) tracking systems that not only achieve ultrahigh spatiotemporal resolution but also provide sufficient working depths suitable for tracking single molecules in 3D tissue models. We then summarize the observables that can be extracted from the trajectory data. Methods to perform single-molecule clustering analysis and future directions are also discussed.
Collapse
Affiliation(s)
- Trung Duc Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Limin H Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
- Texas Materials Institute, University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
4
|
Xie J, Herr S, Ma D, Wu S, Zhao H, Sun S, Ma Z, Chan MYL, Li K, Yang Y, Huang F, Shi R, Yuan C. Acute Transcriptomic and Epigenetic Alterations at T12 After Rat T10 Spinal Cord Contusive Injury. Mol Neurobiol 2023; 60:2937-2953. [PMID: 36750527 DOI: 10.1007/s12035-023-03250-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023]
Abstract
Spinal cord injury is a severely debilitating condition affecting a significant population in the USA. Spinal cord injury patients often have increased risk of developing persistent neuropathic pain and other neurodegenerative conditions beyond the primary lesion center later in their life. The molecular mechanism conferring to the "latent" damages at distal tissues, however, remains elusive. Here, we studied molecular changes conferring abnormal functionality at distal spinal cord (T12) beyond the lesion center (T10) by combining next-generation sequencing (RNA- and bisulfite sequencing), super-resolution microscopy, and immunofluorescence staining at 7 days post injury. We observed significant transcriptomic changes primarily enriched in neuroinflammation and synaptogenesis associated pathways. Transcription factors (TFs) that regulate neurogenesis and neuron plasticity, including Egr1, Klf4, and Myc, are significantly upregulated. Along with global changes in chromatin arrangements and DNA methylation, including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), bisulfite sequencing further reveals the involvement of DNA methylation changes in regulating cytokine, growth factor, and ion channel expression. Collectively, our results pave the way towards understanding transcriptomic and epigenomic mechanism in conferring long-term disease risks at distal tissues away from the primary lesion center and shed light on potential molecular targets that govern the regulatory mechanism at distal spinal cord tissues.
Collapse
Affiliation(s)
- Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Seth Herr
- Center for Paralysis Research, Purdue University, West Lafayette, IN, USA
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, USA
| | - Donghan Ma
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Shichen Wu
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Han Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Siyuan Sun
- Center for Paralysis Research, Purdue University, West Lafayette, IN, USA
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, USA
| | - Zhixiong Ma
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Matthew Yan-Lok Chan
- Agriculture and Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - Katherine Li
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Yang Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Fang Huang
- Agriculture and Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - Riyi Shi
- Center for Paralysis Research, Purdue University, West Lafayette, IN, USA.
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, USA.
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA.
- Purdue Center of Cancer Research, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
5
|
Nieves DJ, Pike JA, Levet F, Williamson DJ, Baragilly M, Oloketuyi S, de Marco A, Griffié J, Sage D, Cohen EAK, Sibarita JB, Heilemann M, Owen DM. A framework for evaluating the performance of SMLM cluster analysis algorithms. Nat Methods 2023; 20:259-267. [PMID: 36765136 DOI: 10.1038/s41592-022-01750-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/06/2022] [Indexed: 02/12/2023]
Abstract
Single-molecule localization microscopy (SMLM) generates data in the form of coordinates of localized fluorophores. Cluster analysis is an attractive route for extracting biologically meaningful information from such data and has been widely applied. Despite a range of cluster analysis algorithms, there exists no consensus framework for the evaluation of their performance. Here, we use a systematic approach based on two metrics to score the success of clustering algorithms in simulated conditions mimicking experimental data. We demonstrate the framework using seven diverse analysis algorithms: DBSCAN, ToMATo, KDE, FOCAL, CAML, ClusterViSu and SR-Tesseler. Given that the best performer depended on the underlying distribution of localizations, we demonstrate an analysis pipeline based on statistical similarity measures that enables the selection of the most appropriate algorithm, and the optimized analysis parameters for real SMLM data. We propose that these standard simulated conditions, metrics and analysis pipeline become the basis for future analysis algorithm development and evaluation.
Collapse
Affiliation(s)
- Daniel J Nieves
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
| | - Jeremy A Pike
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Florian Levet
- Interdisciplinary Institute for Neuroscience, CNRS, IINS, UMR 5297, Université de Bordeaux, Bordeaux, France.,Bordeaux Imaging Center, CNRS, INSERM, BIC, UMS 3420, US 4, Université de Bordeaux, Bordeaux, France
| | - David J Williamson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Mohammed Baragilly
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Department of Mathematics, Insurance and Applied Statistics, Helwan University, Helwan, Egypt
| | - Sandra Oloketuyi
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Rožna Dolina, Slovenia
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Rožna Dolina, Slovenia
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Daniel Sage
- Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Jean-Baptiste Sibarita
- Interdisciplinary Institute for Neuroscience, CNRS, IINS, UMR 5297, Université de Bordeaux, Bordeaux, France
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK. .,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK. .,School of Mathematics, University of Birmingham, Birmingham, UK.
| |
Collapse
|
6
|
Chen L, Liu Q, Chou KC. Human-vision-inspired cluster identification for single-molecule localization microscopy. OPTICS EXPRESS 2023; 31:3459-3466. [PMID: 36785338 DOI: 10.1364/oe.476486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Single-molecule localization microscopy has enabled scientists to visualize cellular structures at the nanometer scale. However, researchers are facing great challenges in analyzing images presented by point clouds. Existing algorithms for cluster identification are coordinate-based analyses requiring users to input cutoff thresholds based on the distance or density of the point cloud. These thresholds are often one's best guess with repeated visual inspections, making the cluster assignment user-dependent. Here, we present a cluster identification algorithm mimicking the modulation transfer function of human vision. This approach does not require any input parameters and produces visually satisfactory cluster assignments. We tested this algorithm by identifying the clusters of the fusion proteins of the Nipah virus on its host cells. This algorithm was further extended to analyze three-dimensional point clouds using virus-like particles as an example.
Collapse
|
7
|
Hyun Y, Kim D. Recent development of computational cluster analysis methods for single-molecule localization microscopy images. Comput Struct Biotechnol J 2023; 21:879-888. [PMID: 36698968 PMCID: PMC9860261 DOI: 10.1016/j.csbj.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/07/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
With the development of super-resolution imaging techniques, it is crucial to understand protein structure at the nanoscale in terms of clustering and organization in a cell. However, cluster analysis from single-molecule localization microscopy (SMLM) images remains challenging because the classical computational cluster analysis methods developed for conventional microscopy images do not apply to pointillism SMLM data, necessitating the development of distinct methods for cluster analysis from SMLM images. In this review, we discuss the development of computational cluster analysis methods for SMLM images by categorizing them into classical and machine-learning-based methods. Finally, we address possible future directions for machine learning-based cluster analysis methods for SMLM data.
Collapse
Affiliation(s)
- Yoonsuk Hyun
- Department of Mathematics, Inha University, Republic of Korea
| | - Doory Kim
- Department of Chemistry, Hanyang University, Republic of Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Republic of Korea
- Institute of Nano Science and Technology, Hanyang University, Republic of Korea
- Research Institute for Natural Sciences, Hanyang University, Republic of Korea
| |
Collapse
|
8
|
Verzelli P, Nold A, Sun C, Heilemann M, Schuman EM, Tchumatchenko T. Unbiased choice of global clustering parameters for single-molecule localization microscopy. Sci Rep 2022. [PMID: 36581654 DOI: 10.1101/2021.02.22.432198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Single-molecule localization microscopy resolves objects below the diffraction limit of light via sparse, stochastic detection of target molecules. Single molecules appear as clustered detection events after image reconstruction. However, identification of clusters of localizations is often complicated by the spatial proximity of target molecules and by background noise. Clustering results of existing algorithms often depend on user-generated training data or user-selected parameters, which can lead to unintentional clustering errors. Here we suggest an unbiased algorithm (FINDER) based on adaptive global parameter selection and demonstrate that the algorithm is robust to noise inclusion and target molecule density. We benchmarked FINDER against the most common density based clustering algorithms in test scenarios based on experimental datasets. We show that FINDER can keep the number of false positive inclusions low while also maintaining a low number of false negative detections in densely populated regions.
Collapse
Affiliation(s)
- Pietro Verzelli
- Institute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany
| | - Andreas Nold
- Institute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany
- Theory of Neural Dynamics Group, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Chao Sun
- Department of Synaptic Plasticity, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Erin M Schuman
- Department of Synaptic Plasticity, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Tatjana Tchumatchenko
- Institute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany.
- Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.
- Theory of Neural Dynamics Group, Max Planck Institute for Brain Research, Frankfurt, Germany.
| |
Collapse
|
9
|
Verzelli P, Nold A, Sun C, Heilemann M, Schuman EM, Tchumatchenko T. Unbiased choice of global clustering parameters for single-molecule localization microscopy. Sci Rep 2022; 12:22561. [PMID: 36581654 PMCID: PMC9800574 DOI: 10.1038/s41598-022-27074-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
Single-molecule localization microscopy resolves objects below the diffraction limit of light via sparse, stochastic detection of target molecules. Single molecules appear as clustered detection events after image reconstruction. However, identification of clusters of localizations is often complicated by the spatial proximity of target molecules and by background noise. Clustering results of existing algorithms often depend on user-generated training data or user-selected parameters, which can lead to unintentional clustering errors. Here we suggest an unbiased algorithm (FINDER) based on adaptive global parameter selection and demonstrate that the algorithm is robust to noise inclusion and target molecule density. We benchmarked FINDER against the most common density based clustering algorithms in test scenarios based on experimental datasets. We show that FINDER can keep the number of false positive inclusions low while also maintaining a low number of false negative detections in densely populated regions.
Collapse
Affiliation(s)
- Pietro Verzelli
- grid.15090.3d0000 0000 8786 803XInstitute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany
| | - Andreas Nold
- grid.15090.3d0000 0000 8786 803XInstitute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany ,grid.419505.c0000 0004 0491 3878Theory of Neural Dynamics Group, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Chao Sun
- grid.419505.c0000 0004 0491 3878Department of Synaptic Plasticity, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Mike Heilemann
- grid.7839.50000 0004 1936 9721Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Erin M. Schuman
- grid.419505.c0000 0004 0491 3878Department of Synaptic Plasticity, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Tatjana Tchumatchenko
- grid.15090.3d0000 0000 8786 803XInstitute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany ,grid.410607.4Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany ,grid.419505.c0000 0004 0491 3878Theory of Neural Dynamics Group, Max Planck Institute for Brain Research, Frankfurt, Germany
| |
Collapse
|
10
|
Fazel M, Wester MJ, Schodt DJ, Cruz SR, Strauss S, Schueder F, Schlichthaerle T, Gillette JM, Lidke DS, Rieger B, Jungmann R, Lidke KA. High-precision estimation of emitter positions using Bayesian grouping of localizations. Nat Commun 2022; 13:7152. [PMID: 36418347 PMCID: PMC9684143 DOI: 10.1038/s41467-022-34894-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
Single-molecule localization microscopy super-resolution methods rely on stochastic blinking/binding events, which often occur multiple times from each emitter over the course of data acquisition. Typically, the blinking/binding events from each emitter are treated as independent events, without an attempt to assign them to a particular emitter. Here, we describe a Bayesian method of inferring the positions of the tagged molecules by exploring the possible grouping and combination of localizations from multiple blinking/binding events. The results are position estimates of the tagged molecules that have improved localization precision and facilitate nanoscale structural insights. The Bayesian framework uses the localization precisions to learn the statistical distribution of the number of blinking/binding events per emitter and infer the number and position of emitters. We demonstrate the method on a range of synthetic data with various emitter densities, DNA origami constructs and biological structures using DNA-PAINT and dSTORM data. We show that under some experimental conditions it is possible to achieve sub-nanometer precision.
Collapse
Affiliation(s)
- Mohamadreza Fazel
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Michael J Wester
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM, USA
| | - David J Schodt
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Sebastian Restrepo Cruz
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - Sebastian Strauss
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Schueder
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Thomas Schlichthaerle
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jennifer M Gillette
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Diane S Lidke
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Bernd Rieger
- Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands
| | - Ralf Jungmann
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA.
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA.
| |
Collapse
|
11
|
Saavedra LA, Buena-Maizón H, Barrantes FJ. Mapping the Nicotinic Acetylcholine Receptor Nanocluster Topography at the Cell Membrane with STED and STORM Nanoscopies. Int J Mol Sci 2022; 23:ijms231810435. [PMID: 36142349 PMCID: PMC9499342 DOI: 10.3390/ijms231810435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
The cell-surface topography and density of nicotinic acetylcholine receptors (nAChRs) play a key functional role in the synapse. Here we employ in parallel two labeling and two super-resolution microscopy strategies to characterize the distribution of this receptor at the plasma membrane of the mammalian clonal cell line CHO-K1/A5. Cells were interrogated with two targeted techniques (confocal microscopy and stimulated emission depletion (STED) nanoscopy) and single-molecule nanoscopy (stochastic optical reconstruction microscopy, STORM) using the same fluorophore, Alexa Fluor 647, tagged onto either α-bungarotoxin (BTX) or the monoclonal antibody mAb35. Analysis of the topography of nanometer-sized aggregates (“nanoclusters”) was carried out using STORMGraph, a quantitative clustering analysis for single-molecule localization microscopy based on graph theory and community detection, and ASTRICS, an inter-cluster similarity algorithm based on computational geometry. Antibody-induced crosslinking of receptors resulted in nanoclusters with a larger number of receptor molecules and higher densities than those observed in BTX-labeled samples. STORM and STED provided complementary information, STED rendering a direct map of the mesoscale nAChR distribution at distances ~10-times larger than the nanocluster centroid distances measured in STORM samples. By applying photon threshold filtering analysis, we show that it is also possible to detect the mesoscale organization in STORM images.
Collapse
|
12
|
Bochenek S, Camerin F, Zaccarelli E, Maestro A, Schmidt MM, Richtering W, Scotti A. In-situ study of the impact of temperature and architecture on the interfacial structure of microgels. Nat Commun 2022; 13:3744. [PMID: 35768399 PMCID: PMC9243037 DOI: 10.1038/s41467-022-31209-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022] Open
Abstract
The structural characterization of microgels at interfaces is fundamental to understand both their 2D phase behavior and their role as stabilizers that enable emulsions to be broken on demand. However, this characterization is usually limited by available experimental techniques, which do not allow a direct investigation at interfaces. To overcome this difficulty, here we employ neutron reflectometry, which allows us to probe the structure and responsiveness of the microgels in-situ at the air-water interface. We investigate two types of microgels with different cross-link density, thus having different softness and deformability, both below and above their volume phase transition temperature, by combining experiments with computer simulations of in silico synthesized microgels. We find that temperature only affects the portion of microgels in water, while the strongest effect of the microgels softness is observed in their ability to protrude into the air. In particular, standard microgels have an apparent contact angle of few degrees, while ultra-low cross-linked microgels form a flat polymeric layer with zero contact angle. Altogether, this study provides an in-depth microscopic description of how different microgel architectures affect their arrangements at interfaces, and will be the foundation for a better understanding of their phase behavior and assembly.
Collapse
Affiliation(s)
- Steffen Bochenek
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
| | - Fabrizio Camerin
- CNR-ISC, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185, Roma, Italy.,Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185, Roma, Italy
| | - Emanuela Zaccarelli
- CNR-ISC, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185, Roma, Italy.,Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185, Roma, Italy
| | - Armando Maestro
- Institut Laue-Langevin ILL DS/LSS, 71 Avenue des Martyrs, 38000, Grenoble, France.,Centro de Fısica de Materiales (CSIC, UPV/EHU) - Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, 20018, San Sebastián, Spain.,IKERBASQUE-Basque Foundation for Science, Plaza Euskadi 5, 48009, Bilbao, Spain
| | - Maximilian M Schmidt
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
| | - Walter Richtering
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
| | - Andrea Scotti
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany.
| |
Collapse
|
13
|
Scotti A, Schulte MF, Lopez CG, Crassous JJ, Bochenek S, Richtering W. How Softness Matters in Soft Nanogels and Nanogel Assemblies. Chem Rev 2022; 122:11675-11700. [PMID: 35671377 DOI: 10.1021/acs.chemrev.2c00035] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Softness plays a key role in determining the macroscopic properties of colloidal systems, from synthetic nanogels to biological macromolecules, from viruses to star polymers. However, we are missing a way to quantify what the term "softness" means in nanoscience. Having quantitative parameters is fundamental to compare different systems and understand what the consequences of softness on the macroscopic properties are. Here, we propose different quantities that can be measured using scattering methods and microscopy experiments. On the basis of these quantities, we review the recent literature on micro- and nanogels, i.e. cross-linked polymer networks swollen in water, a widely used model system for soft colloids. Applying our criteria, we address the question what makes a nanomaterial soft? We discuss and introduce general criteria to quantify the different definitions of softness for an individual compressible colloid. This is done in terms of the energetic cost associated with the deformation and the capability of the colloid to isotropically deswell. Then, concentrated solutions of soft colloids are considered. New definitions of softness and new parameters, which depend on the particle-to-particle interactions, are introduced in terms of faceting and interpenetration. The influence of the different synthetic routes on the softness of nanogels is discussed. Concentrated solutions of nanogels are considered and we review the recent results in the literature concerning the phase behavior and flow properties of nanogels both in three and two dimensions, in the light of the different parameters we defined. The aim of this review is to look at the results on micro- and nanogels in a more quantitative way that allow us to explain the reported properties in terms of differences in colloidal softness. Furthermore, this review can give researchers dealing with soft colloids quantitative methods to define unambiguously which softness matters in their compound.
Collapse
Affiliation(s)
- Andrea Scotti
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany, European Union
| | - M Friederike Schulte
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany, European Union
| | - Carlos G Lopez
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany, European Union
| | - Jérôme J Crassous
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany, European Union
| | - Steffen Bochenek
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany, European Union
| | - Walter Richtering
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany, European Union
| |
Collapse
|
14
|
Jensen LG, Hoh TY, Williamson DJ, Griffié J, Sage D, Rubin-Delanchy P, Owen DM. Correction of multiple-blinking artifacts in photoactivated localization microscopy. Nat Methods 2022; 19:594-602. [PMID: 35545712 DOI: 10.1038/s41592-022-01463-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 03/18/2022] [Indexed: 11/09/2022]
Abstract
Photoactivated localization microscopy (PALM) produces an array of localization coordinates by means of photoactivatable fluorescent proteins. However, observations are subject to fluorophore multiple blinking and each protein is included in the dataset an unknown number of times at different positions, due to localization error. This causes artificial clustering to be observed in the data. We present a 'model-based correction' (MBC) workflow using calibration-free estimation of blinking dynamics and model-based clustering to produce a corrected set of localization coordinates representing the true underlying fluorophore locations with enhanced localization precision, outperforming the state of the art. The corrected data can be reliably tested for spatial randomness or analyzed by other clustering approaches, and descriptors such as the absolute number of fluorophores per cluster are now quantifiable, which we validate with simulated data and experimental data with known ground truth. Using MBC, we confirm that the adapter protein, the linker for activation of T cells, is clustered at the T cell immunological synapse.
Collapse
Affiliation(s)
- Louis G Jensen
- Department of Mathematics, Aarhus University, Aarhus, Denmark.
| | - Tjun Yee Hoh
- Institute for Statistical Science, School of Mathematics, University of Bristol, Bristol, UK
| | - David J Williamson
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of Physics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Daniel Sage
- Biomedical Imaging Group, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Patrick Rubin-Delanchy
- Institute for Statistical Science, School of Mathematics, University of Bristol, Bristol, UK.
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, School of Mathematics and Centre of Membrane Proteins and Receptors, University of Birmingham, Birmingham, UK.
| |
Collapse
|
15
|
A coordinate-based co-localization index to quantify and visualize spatial associations in single-molecule localization microscopy. Sci Rep 2022; 12:4676. [PMID: 35304545 PMCID: PMC8933590 DOI: 10.1038/s41598-022-08746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/07/2022] [Indexed: 11/09/2022] Open
Abstract
Visualizing the subcellular distribution of proteins and determining whether specific proteins co-localize is one of the main strategies in determining the organization and potential interactions of protein complexes in biological samples. The development of super-resolution microscopy techniques such as single-molecule localization microscopy (SMLM) has tremendously increased the ability to resolve protein distribution at nanometer resolution. As super-resolution imaging techniques are becoming instrumental in revealing novel biological insights, new quantitative approaches that exploit the unique nature of SMLM datasets are required. Here, we present a new, local density-based algorithm to quantify co-localization in dual-color SMLM datasets. We show that this method is broadly applicable and only requires molecular coordinates and their localization precision as inputs. Using simulated point patterns, we show that this method robustly measures the co-localization in dual-color SMLM datasets, independent of localization density, but with high sensitivity towards local enrichments. We further validated our method using SMLM imaging of the microtubule network in epithelial cells and used it to study the spatial association between proteins at neuronal synapses. Together, we present a simple and easy-to-use, but powerful method to analyze the spatial association of molecules in dual-color SMLM datasets.
Collapse
|
16
|
Schneider MC, Schütz GJ. Don’t Be Fooled by Randomness: Valid p-Values for Single Molecule Microscopy. FRONTIERS IN BIOINFORMATICS 2022; 2:811053. [PMID: 36304307 PMCID: PMC9580918 DOI: 10.3389/fbinf.2022.811053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/12/2022] [Indexed: 12/04/2022] Open
Abstract
The human mind shows extraordinary capability at recognizing patterns, while at the same time tending to underestimate the natural scope of random processes. Taken together, this easily misleads researchers in judging whether the observed characteristics of their data are of significance or just the outcome of random effects. One of the best tools to assess whether observed features fall into the scope of pure randomness is statistical significance testing, which quantifies the probability to falsely reject a chosen null hypothesis. The central parameter in this context is the p-value, which can be calculated from the recorded data sets. In case of p-values smaller than the level of significance, the null hypothesis is rejected, otherwise not. While significance testing has found widespread application in many sciences including the life sciences, it is hardly used in (bio-)physics. We propose here that significance testing provides an important and valid addendum to the toolbox of quantitative (single molecule) biology. It allows to support a quantitative judgement (the hypothesis) about the data set with a probabilistic assessment. In this manuscript we describe ways for obtaining valid p-values in two selected applications of single molecule microscopy: (i) Nanoclustering in single molecule localization microscopy. Previously, we developed a method termed 2-CLASTA, which allows to calculate a valid p-value for the null hypothesis of an underlying random distribution of molecules of interest while circumventing overcounting issues. Here, we present an extension to this approach, yielding a single overall p-value for data pooled from multiple cells or experiments. (ii) Single molecule trajectories. Data from a single molecule trajectory are inherently correlated, thus prohibiting a direct analysis via conventional statistical tools. Here, we introduce a block permutation test, which yields a valid p-value for the analysis and comparison of single molecule trajectory data. We exemplify the approach based on FRET trajectories.
Collapse
|
17
|
Bond C, Santiago-Ruiz AN, Tang Q, Lakadamyali M. Technological advances in super-resolution microscopy to study cellular processes. Mol Cell 2022; 82:315-332. [PMID: 35063099 PMCID: PMC8852216 DOI: 10.1016/j.molcel.2021.12.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 01/22/2023]
Abstract
Since its initial demonstration in 2000, far-field super-resolution light microscopy has undergone tremendous technological developments. In parallel, these developments have opened a new window into visualizing the inner life of cells at unprecedented levels of detail. Here, we review the technical details behind the most common implementations of super-resolution microscopy and highlight some of the recent, promising advances in this field.
Collapse
Affiliation(s)
- Charles Bond
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adriana N. Santiago-Ruiz
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qing Tang
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Correspondence should be sent to M.L.:
| |
Collapse
|
18
|
Steindel M, Orsine de Almeida I, Strawbridge S, Chernova V, Holcman D, Ponjavic A, Basu S. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy. Methods Mol Biol 2022; 2476:209-247. [PMID: 35635707 DOI: 10.1007/978-1-0716-2221-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single-molecule localization microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal "snapshots" of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination, 3D SMLM, and protein labeling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analyzing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely, or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
Collapse
Affiliation(s)
- Maike Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Stanley Strawbridge
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Valentyna Chernova
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - David Holcman
- Group of Computational Biology and Applied Mathematics, Institute of Biology, Ecole Normale Supérieure, Paris, France
| | - Aleks Ponjavic
- School of Physics and Astronomy and School of Food Science and Nutrition, University of Leeds, Leeds, UK.
| | - Srinjan Basu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| |
Collapse
|
19
|
Wakefield DL, Tobin SJ, Schmolze D, Jovanovic-Talisman T. Molecular Imaging of HER2 in Patient Tissues with Touch Prep-Quantitative Single Molecule Localization Microscopy. Methods Mol Biol 2022; 2394:231-248. [PMID: 35094332 PMCID: PMC9121336 DOI: 10.1007/978-1-0716-1811-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Biomolecules can be investigated at the nanoscale with quantitative single molecule localization microscopy (qSMLM). This technique, which achieves single molecule sensitivity, can probe how membrane receptors are organized under both normal and pathological conditions. While a number of receptors have been extensively studied in cultured cells, technical challenges have largely impeded their robust quantification in tissue samples. To rigorously interrogate tissue samples, methodological advancements are needed in three areas: analytical preparation of the sample, proper characterization of fluorescent reporters, and rapid/unbiased data analysis. Towards these ends, we have combined qSMLM with a touch preparation technique (touch prep-qSMLM). In this new method, touch prep is first used to obtain monolayers of patient cells. Then, highly selective, fluorescently labeled probes are used to detect the receptors of interest on the plasma membranes of cells. Finally, quantitative algorithms are used to analyze the imaging data. Using this touch prep-qSMLM methodology, we interrogated the density and nano-organization of human epidermal growth factor receptor 2 (HER2) in fresh breast cancer tissues. Touch prep-qSMLM agreed well with current clinical methods. Importantly, touch prep-qSMLM can be easily extended to other pathological conditions and ultimately used in precision medicine.
Collapse
Affiliation(s)
- Devin L Wakefield
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Amgen, South San Francisco, CA, USA
| | - Steven J Tobin
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Daniel Schmolze
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Tijana Jovanovic-Talisman
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
| |
Collapse
|
20
|
Gabitto MI, Marie-Nelly H, Pakman A, Pataki A, Darzacq X, Jordan MI. A Bayesian nonparametric approach to super-resolution single-molecule localization. Ann Appl Stat 2021. [DOI: 10.1214/21-aoas1441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | - Herve Marie-Nelly
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley
| | - Ari Pakman
- Department of Statistics and Center for Theretical Neuroscience, Columbia University
| | - Andras Pataki
- Center for Computational Biology, Flatiron Institute, Simons Foundation
| | - Xavier Darzacq
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley
| | | |
Collapse
|
21
|
Feher K, Graus MS, Coelho S, Farrell MV, Goyette J, Gaus K. K-Neighbourhood Analysis: A Method for Understanding SMLM Images as Compositions of Local Neighbourhoods. FRONTIERS IN BIOINFORMATICS 2021; 1:724127. [PMID: 36303786 PMCID: PMC9581049 DOI: 10.3389/fbinf.2021.724127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 10/04/2021] [Indexed: 11/30/2022] Open
Abstract
Single molecule localisation microscopy (SMLM) is a powerful tool that has revealed the spatial arrangement of cell surface signalling proteins, producing data of enormous complexity. The complexity is partly driven by the convolution of technical and biological signal components, and partly by the challenge of pooling information across many distinct cells. To address these two particular challenges, we have devised a novel algorithm called K-neighbourhood analysis (KNA), which emphasises the fact that each image can also be viewed as a composition of local neighbourhoods. KNA is based on a novel transformation, spatial neighbourhood principal component analysis (SNPCA), which is defined by the PCA of the normalised K-nearest neighbour vectors of a spatially random point pattern. Here, we use KNA to define a novel visualisation of individual images, to compare within and between groups of images and to investigate the preferential patterns of phosphorylation. This methodology is also highly flexible and can be used to augment existing clustering methods by providing clustering diagnostics as well as revealing substructure within microclusters. In summary, we have presented a highly flexible analysis tool that presents new conceptual possibilities in the analysis of SMLM images.
Collapse
Affiliation(s)
- Kristen Feher
- School of Medical Sciences, EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, NSW, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Matthew S. Graus
- School of Medical Sciences, EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, NSW, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Simao Coelho
- School of Medical Sciences, EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, NSW, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Megan V. Farrell
- School of Medical Sciences, EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, NSW, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Jesse Goyette
- School of Medical Sciences, EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, NSW, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Katharina Gaus
- School of Medical Sciences, EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, NSW, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
22
|
Kutz S, Zehrer AC, Svetlitckii R, Gülcüler Balta GS, Galli L, Kleber S, Rentsch J, Martin-Villalba A, Ewers H. An Efficient GUI-Based Clustering Software for Simulation and Bayesian Cluster Analysis of Single-Molecule Localization Microscopy Data. FRONTIERS IN BIOINFORMATICS 2021; 1:723915. [PMID: 36303736 PMCID: PMC9581037 DOI: 10.3389/fbinf.2021.723915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
Ligand binding of membrane proteins triggers many important cellular signaling events by the lateral aggregation of ligand-bound and other membrane proteins in the plane of the plasma membrane. This local clustering can lead to the co-enrichment of molecules that create an intracellular signal or bring sufficient amounts of activity together to shift an existing equilibrium towards the execution of a signaling event. In this way, clustering can serve as a cellular switch. The underlying uneven distribution and local enrichment of the signaling cluster’s constituting membrane proteins can be used as a functional readout. This information is obtained by combining single-molecule fluorescence microscopy with cluster algorithms that can reliably and reproducibly distinguish clusters from fluctuations in the background noise to generate quantitative data on this complex process. Cluster analysis of single-molecule fluorescence microscopy data has emerged as a proliferative field, and several algorithms and software solutions have been put forward. However, in most cases, such cluster algorithms require multiple analysis parameters to be defined by the user, which may lead to biased results. Furthermore, most cluster algorithms neglect the individual localization precision connected to every localized molecule, leading to imprecise results. Bayesian cluster analysis has been put forward to overcome these problems, but so far, it has entailed high computational cost, increasing runtime drastically. Finally, most software is challenging to use as they require advanced technical knowledge to operate. Here we combined three advanced cluster algorithms with the Bayesian approach and parallelization in a user-friendly GUI and achieved up to an order of magnitude faster processing than for previous approaches. Our work will simplify access to a well-controlled analysis of clustering data generated by SMLM and significantly accelerate data processing. The inclusion of a simulation mode aids in the design of well-controlled experimental assays.
Collapse
Affiliation(s)
- Saskia Kutz
- Institut für Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Ando C. Zehrer
- Institut für Biochemie, Freie Universität Berlin, Berlin, Germany
| | | | - Gülce S. Gülcüler Balta
- Department of Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lucrezia Galli
- Department of Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Susanne Kleber
- Department of Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jakob Rentsch
- Institut für Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Ana Martin-Villalba
- Department of Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Helge Ewers
- Institut für Biochemie, Freie Universität Berlin, Berlin, Germany
- *Correspondence: Helge Ewers,
| |
Collapse
|
23
|
Rapid statistical discrimination of fluorescence images of T cell receptors on immobilizing surfaces with different coating conditions. Sci Rep 2021; 11:15488. [PMID: 34326382 PMCID: PMC8322097 DOI: 10.1038/s41598-021-94730-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/15/2021] [Indexed: 11/24/2022] Open
Abstract
The spatial organization of T cell receptors (TCRs) correlates with membrane-associated signal amplification, dispersion, and regulation during T cell activation. Despite its potential clinical importance, quantitative analysis of the spatial arrangement of TCRs from standard fluorescence images remains difficult. Here, we report Statistical Classification Analyses of Membrane Protein Images or SCAMPI as a technique capable of analyzing the spatial arrangement of TCRs on the plasma membrane of T cells. We leveraged medical image analysis techniques that utilize pixel-based values. We transformed grayscale pixel values from fluorescence images of TCRs into estimated model parameters of partial differential equations. The estimated model parameters enabled an accurate classification using linear discrimination techniques, including Fisher Linear Discriminant (FLD) and Logistic Regression (LR). In a proof-of-principle study, we modeled and discriminated images of fluorescently tagged TCRs from Jurkat T cells on uncoated cover glass surfaces (Null) or coated cover glass surfaces with either positively charged poly-L-lysine (PLL) or TCR cross-linking anti-CD3 antibodies (OKT3). Using 80 training images and 20 test images per class, our statistical technique achieved 85% discrimination accuracy for both OKT3 versus PLL and OKT3 versus Null conditions. The run time of image data download, model construction, and image discrimination was 21.89 s on a laptop computer, comprised of 20.43 s for image data download, 1.30 s on the FLD-SCAMPI analysis, and 0.16 s on the LR-SCAMPI analysis. SCAMPI represents an alternative approach to morphology-based qualifications for discriminating complex patterns of membrane proteins conditioned on a small sample size and fast runtime. The technique paves pathways to characterize various physiological and pathological conditions using the spatial organization of TCRs from patient T cells.
Collapse
|
24
|
Fischer LS, Klingner C, Schlichthaerle T, Strauss MT, Böttcher R, Fässler R, Jungmann R, Grashoff C. Quantitative single-protein imaging reveals molecular complex formation of integrin, talin, and kindlin during cell adhesion. Nat Commun 2021; 12:919. [PMID: 33568673 PMCID: PMC7876120 DOI: 10.1038/s41467-021-21142-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/12/2021] [Indexed: 12/21/2022] Open
Abstract
Single-molecule localization microscopy (SMLM) enabling the investigation of individual proteins on molecular scales has revolutionized how biological processes are analysed in cells. However, a major limitation of imaging techniques reaching single-protein resolution is the incomplete and often unknown labeling and detection efficiency of the utilized molecular probes. As a result, fundamental processes such as complex formation of distinct molecular species cannot be reliably quantified. Here, we establish a super-resolution microscopy framework, called quantitative single-molecule colocalization analysis (qSMCL), which permits the identification of absolute molecular quantities and thus the investigation of molecular-scale processes inside cells. The method combines multiplexed single-protein resolution imaging, automated cluster detection, in silico data simulation procedures, and widely applicable experimental controls to determine absolute fractions and spatial coordinates of interacting species on a true molecular level, even in highly crowded subcellular structures. The first application of this framework allowed the identification of a long-sought ternary adhesion complex—consisting of talin, kindlin and active β1-integrin—that specifically forms in cell-matrix adhesion sites. Together, the experiments demonstrate that qSMCL allows an absolute quantification of multiplexed SMLM data and thus should be useful for investigating molecular mechanisms underlying numerous processes in cells. Single-molecule localisation microscopy is limited by low labeling and detection efficiencies of the molecular probes. Here the authors report a framework to obtain absolute molecular quantities on a true molecular scale; the data reveal a ternary adhesion complex underlying cell-matrix adhesion.
Collapse
Affiliation(s)
- Lisa S Fischer
- Department of Quantitative Cell Biology, Institute of Molecular Cell Biology, University of Münster, Münster, Germany.,Group of Molecular Mechanotransduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christoph Klingner
- Department of Quantitative Cell Biology, Institute of Molecular Cell Biology, University of Münster, Münster, Germany.,Group of Molecular Mechanotransduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Research Group Molecular Imaging and Bionanotechnology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maximilian T Strauss
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany.,Research Group Molecular Imaging and Bionanotechnology, Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ralph Böttcher
- Department of Molecular Medicine, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Reinhard Fässler
- Department of Molecular Medicine, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, LMU Munich, Munich, Germany. .,Research Group Molecular Imaging and Bionanotechnology, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Carsten Grashoff
- Department of Quantitative Cell Biology, Institute of Molecular Cell Biology, University of Münster, Münster, Germany. .,Group of Molecular Mechanotransduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
| |
Collapse
|
25
|
Ahmad A, Frindel C, Rousseau D. Detecting Differences of Fluorescent Markers Distribution in Single Cell Microscopy: Textural or Pointillist Feature Space? Front Robot AI 2021; 7:39. [PMID: 33501207 PMCID: PMC7805927 DOI: 10.3389/frobt.2020.00039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 03/09/2020] [Indexed: 12/22/2022] Open
Abstract
We consider the detection of change in spatial distribution of fluorescent markers inside cells imaged by single cell microscopy. Such problems are important in bioimaging since the density of these markers can reflect the healthy or pathological state of cells, the spatial organization of DNA, or cell cycle stage. With the new super-resolved microscopes and associated microfluidic devices, bio-markers can be detected in single cells individually or collectively as a texture depending on the quality of the microscope impulse response. In this work, we propose, via numerical simulations, to address detection of changes in spatial density or in spatial clustering with an individual (pointillist) or collective (textural) approach by comparing their performances according to the size of the impulse response of the microscope. Pointillist approaches show good performances for small impulse response sizes only, while all textural approaches are found to overcome pointillist approaches with small as well as with large impulse response sizes. These results are validated with real fluorescence microscopy images with conventional resolution. This, a priori non-intuitive result in the perspective of the quest of super-resolution, demonstrates that, for difference detection tasks in single cell microscopy, super-resolved microscopes may not be mandatory and that lower cost, sub-resolved, microscopes can be sufficient.
Collapse
Affiliation(s)
- Ali Ahmad
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes, UMR INRAE IRHS, Université d'Angers, Angers, France.,Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé, CNRS UMR 5220-INSERM U1206, Université Lyon 1, INSA de Lyon, Lyon, France
| | - Carole Frindel
- Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé, CNRS UMR 5220-INSERM U1206, Université Lyon 1, INSA de Lyon, Lyon, France
| | - David Rousseau
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes, UMR INRAE IRHS, Université d'Angers, Angers, France
| |
Collapse
|
26
|
Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffié J, Manley S, Jungmann R, Sauer M, Lakadamyali M, Zimmer C. Single-molecule localization microscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:39. [PMID: 35663461 PMCID: PMC9160414 DOI: 10.1038/s43586-021-00038-x] [Citation(s) in RCA: 243] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM.
Collapse
Affiliation(s)
- Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
| | - Melina T. Gyparaki
- Department of Biology, University of Pennsylvania,
Philadelphia, PA, USA
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
- ;
;
;
;
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
- ;
;
;
;
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
- ;
;
;
;
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- ;
;
;
;
| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
- ;
;
;
;
| |
Collapse
|
27
|
Multi-color Molecular Visualization of Signaling Proteins Reveals How C-Terminal Src Kinase Nanoclusters Regulate T Cell Receptor Activation. Cell Rep 2020; 33:108523. [PMID: 33357425 DOI: 10.1016/j.celrep.2020.108523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/07/2020] [Accepted: 11/24/2020] [Indexed: 11/22/2022] Open
Abstract
Elucidating the mechanisms that controlled T cell activation requires visualization of the spatial organization of multiple proteins on the submicron scale. Here, we use stoichiometrically accurate, multiplexed, single-molecule super-resolution microscopy (DNA-PAINT) to image the nanoscale spatial architecture of the primary inhibitor of the T cell signaling pathway, Csk, and two binding partners implicated in its membrane association, PAG and TRAF3. Combined with a newly developed co-clustering analysis framework, we find that Csk forms nanoscale clusters proximal to the plasma membrane that are lost post-stimulation and are re-recruited at later time points. Unexpectedly, these clusters do not co-localize with PAG at the membrane but instead provide a ready pool of monomers to downregulate signaling. By generating CRISPR-Cas9 knockout T cells, our data also identify that a major risk factor for autoimmune diseases, the protein tyrosine phosphatase non-receptor type 22 (PTPN22) locus, is essential for Csk nanocluster re-recruitment and for maintenance of the synaptic PAG population.
Collapse
|
28
|
Pike JA, Khan AO, Pallini C, Thomas SG, Mund M, Ries J, Poulter NS, Styles IB. Topological data analysis quantifies biological nano-structure from single molecule localization microscopy. Bioinformatics 2020; 36:1614-1621. [PMID: 31626286 PMCID: PMC7162425 DOI: 10.1093/bioinformatics/btz788] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 09/03/2019] [Accepted: 10/17/2019] [Indexed: 01/23/2023] Open
Abstract
Motivation Localization microscopy data is represented by a set of spatial coordinates, each corresponding to a single detection, that form a point cloud. This can be analyzed either by rendering an image from these coordinates, or by analyzing the point cloud directly. Analysis of this type has focused on clustering detections into distinct groups which produces measurements such as cluster area, but has limited capacity to quantify complex molecular organization and nano-structure. Results We present a segmentation protocol which, through the application of persistence-based clustering, is capable of probing densely packed structures which vary in scale. An increase in segmentation performance over state-of-the-art methods is demonstrated. Moreover we employ persistent homology to move beyond clustering, and quantify the topological structure within data. This provides new information about the preserved shapes formed by molecular architecture. Our methods are flexible and we demonstrate this by applying them to receptor clustering in platelets, nuclear pore components, endocytic proteins and microtubule networks. Both 2D and 3D implementations are provided within RSMLM, an R package for pointillist-based analysis and batch processing of localization microscopy data. Availability and implementation RSMLM has been released under the GNU General Public License v3.0 and is available at https://github.com/JeremyPike/RSMLM. Tutorials for this library implemented as Binder ready Jupyter notebooks are available at https://github.com/JeremyPike/RSMLM-tutorials. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Jeremy A Pike
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Abdullah O Khan
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Chiara Pallini
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Steven G Thomas
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Markus Mund
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany.,Department of Biochemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Natalie S Poulter
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Iain B Styles
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK.,School of Computer Science, University of Birmingham, Birmingham B15 2TT, UK
| |
Collapse
|
29
|
Nosov G, Kahms M, Klingauf J. The Decade of Super-Resolution Microscopy of the Presynapse. Front Synaptic Neurosci 2020; 12:32. [PMID: 32848695 PMCID: PMC7433402 DOI: 10.3389/fnsyn.2020.00032] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 07/21/2020] [Indexed: 01/05/2023] Open
Abstract
The presynaptic compartment of the chemical synapse is a small, yet extremely complex structure. Considering its size, most methods of optical microscopy are not able to resolve its nanoarchitecture and dynamics. Thus, its ultrastructure could only be studied by electron microscopy. In the last decade, new methods of optical superresolution microscopy have emerged allowing the study of cellular structures and processes at the nanometer scale. While this is a welcome addition to the experimental arsenal, it has necessitated careful analysis and interpretation to ensure the data obtained remains artifact-free. In this article we review the application of nanoscopic techniques to the study of the synapse and the progress made over the last decade with a particular focus on the presynapse. We find to our surprise that progress has been limited, calling for imaging techniques and probes that allow dense labeling, multiplexing, longer imaging times, higher temporal resolution, while at least maintaining the spatial resolution achieved thus far.
Collapse
Affiliation(s)
- Georgii Nosov
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany.,CIM-IMPRS Graduate Program in Münster, Münster, Germany
| | - Martin Kahms
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Jurgen Klingauf
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| |
Collapse
|
30
|
Sun Y. Potential quality improvement of stochastic optical localization nanoscopy images obtained by frame by frame localization algorithms. Sci Rep 2020; 10:11844. [PMID: 32678167 PMCID: PMC7367355 DOI: 10.1038/s41598-020-68564-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/26/2020] [Indexed: 12/28/2022] Open
Abstract
A data movie of stochastic optical localization nanoscopy contains spatial and temporal correlations, both providing information of emitter locations. The majority of localization algorithms in the literature estimate emitter locations by frame-by-frame localization (FFL), which exploit only the spatial correlation and leave the temporal correlation into the FFL nanoscopy images. The temporal correlation contained in the FFL images, if exploited, can improve the localization accuracy and the image quality. In this paper, we analyze the properties of the FFL images in terms of root mean square minimum distance (RMSMD) and root mean square error (RMSE). It is shown that RMSMD and RMSE can be potentially reduced by a maximum fold equal to the square root of the average number of activations per emitter. Analyzed and revealed are also several statistical properties of RMSMD and RMSE and their relationship with respect to a large number of data frames, bias and variance of localization errors, small localization errors, sample drift, and the worst FFL image. Numerical examples are taken and the results confirm the prediction of analysis. The ideas about how to develop an algorithm to exploit the temporal correlation of FFL images are also briefly discussed. The results suggest development of two kinds of localization algorithms: the algorithms that can exploit the temporal correlation of FFL images and the unbiased localization algorithms.
Collapse
Affiliation(s)
- Yi Sun
- Electrical Engineering Department, Nanoscopy Laboratory, The City College of City University of New York, New York, NY, 10031, USA.
| |
Collapse
|
31
|
Khater IM, Nabi IR, Hamarneh G. A Review of Super-Resolution Single-Molecule Localization Microscopy Cluster Analysis and Quantification Methods. PATTERNS (NEW YORK, N.Y.) 2020; 1:100038. [PMID: 33205106 PMCID: PMC7660399 DOI: 10.1016/j.patter.2020.100038] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-molecule localization microscopy (SMLM) is a relatively new imaging modality, winning the 2014 Nobel Prize in Chemistry, and considered as one of the key super-resolution techniques. SMLM resolution goes beyond the diffraction limit of light microscopy and achieves resolution on the order of 10-20 nm. SMLM thus enables imaging single molecules and study of the low-level molecular interactions at the subcellular level. In contrast to standard microscopy imaging that produces 2D pixel or 3D voxel grid data, SMLM generates big data of 2D or 3D point clouds with millions of localizations and associated uncertainties. This unprecedented breakthrough in imaging helps researchers employ SMLM in many fields within biology and medicine, such as studying cancerous cells and cell-mediated immunity and accelerating drug discovery. However, SMLM data quantification and interpretation methods have yet to keep pace with the rapid advancement of SMLM imaging. Researchers have been actively exploring new computational methods for SMLM data analysis to extract biosignatures of various biological structures and functions. In this survey, we describe the state-of-the-art clustering methods adopted to analyze and quantify SMLM data and examine the capabilities and shortcomings of the surveyed methods. We classify the methods according to (1) the biological application (i.e., the imaged molecules/structures), (2) the data acquisition (such as imaging modality, dimension, resolution, and number of localizations), and (3) the analysis details (2D versus 3D, field of view versus region of interest, use of machine-learning and multi-scale analysis, biosignature extraction, etc.). We observe that the majority of methods that are based on second-order statistics are sensitive to noise and imaging artifacts, have not been applied to 3D data, do not leverage machine-learning formulations, and are not scalable for big-data analysis. Finally, we summarize state-of-the-art methodology, discuss some key open challenges, and identify future opportunities for better modeling and design of an integrated computational pipeline to address the key challenges.
Collapse
Affiliation(s)
- Ismail M. Khater
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ghassan Hamarneh
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| |
Collapse
|
32
|
Nieves DJ, Owen DM. Analysis methods for interrogating spatial organisation of single molecule localisation microscopy data. Int J Biochem Cell Biol 2020; 123:105749. [PMID: 32325279 DOI: 10.1016/j.biocel.2020.105749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/06/2020] [Accepted: 04/16/2020] [Indexed: 01/01/2023]
Abstract
Single-molecule localisation microscopy (SMLM) gives access to biological information below the diffraction limit, allowing nanoscale cellular structures to be probed. The data output is unlike that of conventional microscopy images, instead consisting of an array of molecular coordinates. These represent a spatial point pattern that attempts to approximate, as closely as possible, the underlying positions of the molecules of interest. Here, we review the analysis methods that can be used to extract biological insight from SMLM data, in particular for the application of quantifying nanoscale molecular clustering. We review how some of the common artefacts inherent in SMLM can corrupt the acquired data, and therefore, how the output of SMLM cluster analysis should be interpreted.
Collapse
Affiliation(s)
- Daniel J Nieves
- Institute of Immunology and Immunotherapy, School of Medical and Dental Sciences and Department of Mathematics, University of Birmingham, Birmingham, B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, B15 2TT, UK
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, School of Medical and Dental Sciences and Department of Mathematics, University of Birmingham, Birmingham, B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, B15 2TT, UK.
| |
Collapse
|
33
|
Machine learning for cluster analysis of localization microscopy data. Nat Commun 2020; 11:1493. [PMID: 32198352 PMCID: PMC7083906 DOI: 10.1038/s41467-020-15293-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 02/27/2020] [Indexed: 12/29/2022] Open
Abstract
Quantifying the extent to which points are clustered in single-molecule localization microscopy data is vital to understanding the spatial relationships between molecules in the underlying sample. Many existing computational approaches are limited in their ability to process large-scale data sets, to deal effectively with sample heterogeneity, or require subjective user-defined analysis parameters. Here, we develop a supervised machine-learning approach to cluster analysis which is fast and accurate. Trained on a variety of simulated clustered data, the neural network can classify millions of points from a typical single-molecule localization microscopy data set, with the potential to include additional classifiers to describe different subtypes of clusters. The output can be further refined for the measurement of cluster area, shape, and point-density. We demonstrate this approach on simulated data and experimental data of the kinase Csk and the adaptor PAG in primary human T cell immunological synapses. The characterization of clusters in single-molecule microscopy data is vital to reconstruct emerging spatial patterns. Here, the authors present a fast and accurate machine-learning approach to clustering, to address the issues related to the size of the data and to sample heterogeneity.
Collapse
|
34
|
Davis JL, Zhang Y, Yi S, Du F, Song KH, Scott EA, Sun C, Zhang HF. Super-Resolution Imaging of Self-Assembled Nanocarriers Using Quantitative Spectroscopic Analysis for Cluster Extraction. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2291-2299. [PMID: 32069413 PMCID: PMC7445082 DOI: 10.1021/acs.langmuir.9b03149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Self-assembled nanocarriers have inspired a range of applications for bioimaging, diagnostics, and drug delivery. The noninvasive visualization and characterization of these nanocarriers are important to understand their structure to function relationship. However, the quantitative visualization of nanocarriers in the sample's native environment remains challenging with the use of existing technologies. Single-molecule localization microscopy (SMLM) has the potential to provide both high-resolution visualization and quantitative analysis of nanocarriers in their native environment. However, nonspecific binding of fluorescent probes used in SMLM can introduce artifacts, which imposes challenges in the quantitative analysis of SMLM images. We showed the feasibility of using spectroscopic point accumulation for imaging in nanoscale topography (sPAINT) to visualize self-assembled polymersomes (PS) with molecular specificity. Furthermore, we analyzed the unique spectral signatures of Nile Red (NR) molecules bound to the PS to reject artifacts from nonspecific NR bindings. We further developed quantitative spectroscopic analysis for cluster extraction (qSPACE) to increase the localization density by 4-fold compared to sPAINT; thus, reducing variations in PS size measurements to less than 5%. Finally, using qSPACE, we quantitatively imaged PS at various concentrations in aqueous solutions with ∼20 nm localization precision and 97% reduction in sample misidentification relative to conventional SMLM.
Collapse
Affiliation(s)
- Janel L. Davis
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Yang Zhang
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Sijia Yi
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Fanfan Du
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Ki-Hee Song
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Evan A. Scott
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Hao F. Zhang
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| |
Collapse
|
35
|
Griffié J, Peters R, Owen DM. An agent-based model of molecular aggregation at the cell membrane. PLoS One 2020; 15:e0226825. [PMID: 32032349 PMCID: PMC7006917 DOI: 10.1371/journal.pone.0226825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/04/2019] [Indexed: 12/22/2022] Open
Abstract
Molecular clustering at the plasma membrane has long been identified as a key process and is associated with regulating signalling pathways across cell types. Recent advances in microscopy, in particular the rise of super-resolution, have allowed the experimental observation of nanoscale molecular clusters in the plasma membrane. However, modelling approaches capable of recapitulating these observations are in their infancy, partly because of the extremely complex array of biophysical factors which influence molecular distributions and dynamics in the plasma membrane. We propose here a highly abstracted approach: an agent-based model dedicated to the study of molecular aggregation at the plasma membrane. We show that when molecules are modelled as though they can act (diffuse) in a manner which is influenced by their molecular neighbourhood, many of the distributions observed in cells can be recapitulated, even though such sensing and response is not possible for real membrane molecules. As such, agent-based offers a unique platform which may lead to a new understanding of how molecular clustering in extremely complex molecular environments can be abstracted, simulated and interpreted using simple rules.
Collapse
Affiliation(s)
- Juliette Griffié
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, London, England, United Kingdom
- * E-mail: (JG); (DO)
| | - Ruby Peters
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, London, England, United Kingdom
| | - Dylan M. Owen
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, London, England, United Kingdom
- * E-mail: (JG); (DO)
| |
Collapse
|
36
|
Košuta T, Cullell-Dalmau M, Cella Zanacchi F, Manzo C. Bayesian analysis of data from segmented super-resolution images for quantifying protein clustering. Phys Chem Chem Phys 2020; 22:1107-1114. [PMID: 31895350 DOI: 10.1039/c9cp05616e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further permits the quantitation relevant parameters to determine the molecular organization and stoichiometry in cells. However, the inherently stochastic nature of fluorescence emission and labeling strategies imposes the use of dedicated methods to accurately estimate these parameters. Here, we describe a Bayesian approach to precisely quantitate the relative abundance of molecular aggregates of different stoichiometry from segmented images. The distribution of proxies for the number of molecules in a cluster, such as the number of localizations or the fluorescence intensity, is fitted via a nested sampling algorithm to compare mixture models of increasing complexity and thus determine the optimum number of mixture components and their weights. We test the performance of the algorithm on in silico data as a function of the number of data points, threshold, and distribution shape. We compare these results to those obtained with other statistical methods, showing the improved performance of our approach. Our method provides a robust tool for model selection in fitting data extracted from fluorescence imaging, thus improving the precision of parameter determination. Importantly, the largest benefit of this method occurs for small-statistics or incomplete datasets, enabling an accurate analysis at the single image level. We further present the results of its application to experimental data obtained from the super-resolution imaging of dynein in HeLa cells, confirming the presence of a mixed population of cytoplasmic single motors and higher-order structures.
Collapse
Affiliation(s)
- Tina Košuta
- The Quantitative BioImaging lab, Facultat de Ciències i Tecnologia, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain. and University of Ljubljana, Ljubljana, Slovenia
| | - Marta Cullell-Dalmau
- The Quantitative BioImaging lab, Facultat de Ciències i Tecnologia, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain.
| | - Francesca Cella Zanacchi
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy and Biophysics Institute (IBF), National Research Council (CNR), Genoa, Italy
| | - Carlo Manzo
- The Quantitative BioImaging lab, Facultat de Ciències i Tecnologia, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain.
| |
Collapse
|
37
|
Hansen AS, Hsieh THS, Cattoglio C, Pustova I, Saldaña-Meyer R, Reinberg D, Darzacq X, Tjian R. Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. Mol Cell 2019; 76:395-411.e13. [PMID: 31522987 PMCID: PMC7251926 DOI: 10.1016/j.molcel.2019.07.039] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/16/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022]
Abstract
Mammalian genomes are folded into topologically associating domains (TADs), consisting of chromatin loops anchored by CTCF and cohesin. Some loops are cell-type specific. Here we asked whether CTCF loops are established by a universal or locus-specific mechanism. Investigating the molecular determinants of CTCF clustering, we found that CTCF self-association in vitro is RNase sensitive and that an internal RNA-binding region (RBRi) mediates CTCF clustering and RNA interaction in vivo. Strikingly, deleting the RBRi impairs about half of all chromatin loops in mESCs and causes deregulation of gene expression. Disrupted loop formation correlates with diminished clustering and chromatin binding of RBRi mutant CTCF, which in turn results in a failure to halt cohesin-mediated extrusion. Thus, CTCF loops fall into at least two classes: RBRi-independent and RBRi-dependent loops. We speculate that evidence for RBRi-dependent loops may provide a molecular mechanism for establishing cell-specific CTCF loops, potentially regulated by RNA(s) or other RBRi-interacting partners.
Collapse
Affiliation(s)
- Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Tsung-Han S Hsieh
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Iryna Pustova
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ricardo Saldaña-Meyer
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Langone Health, New York, NY 10016, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Langone Health, New York, NY 10016, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
| |
Collapse
|
38
|
Shannon MJ, Pineau J, Griffié J, Aaron J, Peel T, Williamson DJ, Zamoyska R, Cope AP, Cornish GH, Owen DM. Differential nanoscale organisation of LFA-1 modulates T-cell migration. J Cell Sci 2019; 133:jcs.232991. [PMID: 31471459 PMCID: PMC7614863 DOI: 10.1242/jcs.232991] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/21/2019] [Indexed: 11/20/2022] Open
Abstract
Effector T-cells rely on integrins to drive adhesion and migration to facilitate their immune function. The heterodimeric transmembrane integrin LFA-1 (αLβ2 integrin) regulates adhesion and migration of effector T-cells through linkage of the extracellular matrix with the intracellular actin treadmill machinery. Here, we quantified the velocity and direction of F-actin flow in migrating T-cells alongside single-molecule localisation of transmembrane and intracellular LFA-1. Results showed that actin retrograde flow positively correlated and immobile actin negatively correlated with T-cell velocity. Plasma membrane-localised LFA-1 forms unique nano-clustering patterns in the leading edge, compared to the mid-focal zone, of migrating T-cells. Deleting the cytosolic phosphatase PTPN22, loss-of-function mutations of which have been linked to autoimmune disease, increased T-cell velocity, and leading-edge co-clustering of pY397 FAK, pY416 Src family kinases and LFA-1. These data suggest that differential nanoclustering patterns of LFA-1 in migrating T-cells may instruct intracellular signalling. Our data presents a paradigm where T-cells modulate the nanoscale organisation of adhesion and signalling molecules to fine tune their migration speed, with implications for the regulation of immune and inflammatory responses.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Michael J Shannon
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
| | - Judith Pineau
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
| | - Juliette Griffié
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
| | - Jesse Aaron
- Advanced Imaging Center, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Tamlyn Peel
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology and Microbiological Sciences, King's College London, London SE1 1UL, UK
| | - David J Williamson
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
| | - Rose Zamoyska
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Andrew P Cope
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology and Microbiological Sciences, King's College London, London SE1 1UL, UK
| | - Georgina H Cornish
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology and Microbiological Sciences, King's College London, London SE1 1UL, UK
| | - Dylan M Owen
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK .,Institute of Immunology and Immunotherapy and Department of Mathematics and Centre for Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham B15 2TQ, UK
| |
Collapse
|
39
|
Andronov L, Michalon J, Ouararhni K, Orlov I, Hamiche A, Vonesch JL, Klaholz BP. 3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations. Bioinformatics 2019; 34:3004-3012. [PMID: 29635310 DOI: 10.1093/bioinformatics/bty200] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 04/02/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Single-molecule localization microscopy (SMLM) can play an important role in integrated structural biology approaches to identify, localize and determine the 3D structure of cellular structures. While many tools exist for the 3D analysis and visualization of crystal or cryo-EM structures little exists for 3D SMLM data, which can provide unique insights but are particularly challenging to analyze in three dimensions especially in a dense cellular context. Results We developed 3DClusterViSu, a method based on 3D Voronoi tessellations that allows local density estimation, segmentation and quantification of 3D SMLM data and visualization of protein clusters within a 3D tool. We show its robust performance on microtubules and histone proteins H2B and CENP-A with distinct spatial distributions. 3DClusterViSu will favor multi-scale and multi-resolution synergies to allow integrating molecular and cellular levels in the analysis of macromolecular complexes. Availability and impementation 3DClusterViSu is available under http://cbi-dev.igbmc.fr/cbi/voronoi3D. Supplementary information Supplementary figures are available at Bioinformatics online.
Collapse
Affiliation(s)
- Leonid Andronov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jonathan Michalon
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Khalid Ouararhni
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Igor Orlov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Ali Hamiche
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jean-Luc Vonesch
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| |
Collapse
|
40
|
Khater IM, Aroca-Ouellette ST, Meng F, Nabi IR, Hamarneh G. Caveolae and scaffold detection from single molecule localization microscopy data using deep learning. PLoS One 2019; 14:e0211659. [PMID: 31449531 PMCID: PMC6709882 DOI: 10.1371/journal.pone.0211659] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022] Open
Abstract
Caveolae are plasma membrane invaginations whose formation requires caveolin-1 (Cav1), the adaptor protein polymerase I, and the transcript release factor (PTRF or CAVIN1). Caveolae have an important role in cell functioning, signaling, and disease. In the absence of CAVIN1/PTRF, Cav1 forms non-caveolar membrane domains called scaffolds. In this work, we train machine learning models to automatically distinguish between caveolae and scaffolds from single molecule localization microscopy (SMLM) data. We apply machine learning algorithms to discriminate biological structures from SMLM data. Our work is the first that is leveraging machine learning approaches (including deep learning models) to automatically identifying biological structures from SMLM data. In particular, we develop and compare three binary classification methods to identify whether or not a given 3D cluster of Cav1 proteins is a caveolae. The first uses a random forest classifier applied to 28 hand-crafted/designed features, the second uses a convolutional neural net (CNN) applied to a projection of the point clouds onto three planes, and the third uses a PointNet model, a recent development that can directly take point clouds as its input. We validate our methods on a dataset of super-resolution microscopy images of PC3 prostate cancer cells labeled for Cav1. Specifically, we have images from two cell populations: 10 PC3 and 10 CAVIN1/PTRF-transfected PC3 cells (PC3-PTRF cells) that form caveolae. We obtained a balanced set of 1714 different cellular structures. Our results show that both the random forest on hand-designed features and the deep learning approach achieve high accuracy in distinguishing the intrinsic features of the caveolae and non-caveolae biological structures. More specifically, both random forest and deep CNN classifiers achieve classification accuracy reaching 94% on our test set, while the PointNet model only reached 83% accuracy. We also discuss the pros and cons of the different approaches.
Collapse
Affiliation(s)
- Ismail M. Khater
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- * E-mail:
| | - Stephane T. Aroca-Ouellette
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Fanrui Meng
- Department of Cellular and Physiological Sciences, LSI Imaging, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, LSI Imaging, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ghassan Hamarneh
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| |
Collapse
|
41
|
Can single molecule localization microscopy detect nanoclusters in T cells? Curr Opin Chem Biol 2019; 51:130-137. [DOI: 10.1016/j.cbpa.2019.05.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/10/2019] [Accepted: 05/21/2019] [Indexed: 11/21/2022]
|
42
|
Hériché JK, Alexander S, Ellenberg J. Integrating Imaging and Omics: Computational Methods and Challenges. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-080917-013328] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescence microscopy imaging has long been complementary to DNA sequencing- and mass spectrometry–based omics in biomedical research, but these approaches are now converging. On the one hand, omics methods are moving from in vitro methods that average across large cell populations to in situ molecular characterization tools with single-cell sensitivity. On the other hand, fluorescence microscopy imaging has moved from a morphological description of tissues and cells to quantitative molecular profiling with single-molecule resolution. Recent technological developments underpinned by computational methods have started to blur the lines between imaging and omics and have made their direct correlation and seamless integration an exciting possibility. As this trend continues rapidly, it will allow us to create comprehensive molecular profiles of living systems with spatial and temporal context and subcellular resolution. Key to achieving this ambitious goal will be novel computational methods and successfully dealing with the challenges of data integration and sharing as well as cloud-enabled big data analysis.
Collapse
Affiliation(s)
- Jean-Karim Hériché
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Stephanie Alexander
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| |
Collapse
|
43
|
The cell wall regulates dynamics and size of plasma-membrane nanodomains in Arabidopsis. Proc Natl Acad Sci U S A 2019; 116:12857-12862. [PMID: 31182605 PMCID: PMC6601011 DOI: 10.1073/pnas.1819077116] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Plant plasma-membrane (PM) proteins are involved in several vital processes, such as detection of pathogens, solute transport, and cellular signaling. For these proteins to function effectively there needs to be structure within the PM allowing, for example, proteins in the same signaling cascade to be spatially organized. Here we demonstrate that several proteins with divergent functions are located in clusters of differing size in the membrane using subdiffraction-limited Airyscan confocal microscopy. Single particle tracking reveals that these proteins move at different rates within the membrane. Actin and microtubule cytoskeletons appear to significantly regulate the mobility of one of these proteins (the pathogen receptor FLS2) and we further demonstrate that the cell wall is critical for the regulation of cluster size by quantifying single particle dynamics of proteins with key roles in morphogenesis (PIN3) and pathogen perception (FLS2). We propose a model in which the cell wall and cytoskeleton are pivotal for regulation of protein cluster size and dynamics, thereby contributing to the formation and functionality of membrane nanodomains.
Collapse
|
44
|
Xu J, Liu Y. A guide to visualizing the spatial epigenome with super-resolution microscopy. FEBS J 2019; 286:3095-3109. [PMID: 31127980 DOI: 10.1111/febs.14938] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/24/2019] [Accepted: 05/23/2019] [Indexed: 12/28/2022]
Abstract
Genomic DNA in eukaryotic cells is tightly compacted with histone proteins into nucleosomes, which are further packaged into the higher-order chromatin structure. The physical structuring of chromatin is highly dynamic and regulated by a large number of epigenetic modifications in response to various environmental exposures, both in normal development and pathological processes such as aging and cancer. Higher-order chromatin structure has been indirectly inferred by conventional bulk biochemical assays on cell populations, which do not allow direct visualization of the spatial information of epigenomics (referred to as spatial epigenomics). With recent advances in super-resolution microscopy, the higher-order chromatin structure can now be visualized in vivo at an unprecedent resolution. This opens up new opportunities to study physical compaction of 3D chromatin structure in single cells, maintaining a well-preserved spatial context of tissue microenvironment. This review discusses the recent application of super-resolution fluorescence microscopy to investigate the higher-order chromatin structure of different epigenomic states. We also envision the synergistic integration of super-resolution microscopy and high-throughput genomic technologies for the analysis of spatial epigenomics to fully understand the genome function in normal biological processes and diseases.
Collapse
Affiliation(s)
- Jianquan Xu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
45
|
Lin R, Clowsley AH, Lutz T, Baddeley D, Soeller C. 3D super-resolution microscopy performance and quantitative analysis assessment using DNA-PAINT and DNA origami test samples. Methods 2019; 174:56-71. [PMID: 31129290 DOI: 10.1016/j.ymeth.2019.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/06/2019] [Accepted: 05/20/2019] [Indexed: 12/29/2022] Open
Abstract
Assessment of the imaging quality in localisation-based super-resolution techniques relies on an accurate characterisation of the imaging setup and analysis procedures. Test samples can provide regular feedback on system performance and facilitate the implementation of new methods. While multiple test samples for regular, 2D imaging are available, they are not common for more specialised imaging modes. Here, we analyse robust test samples for 3D and quantitative super-resolution imaging, which are straightforward to use, are time- and cost-effective and do not require experience beyond basic laboratory and imaging skills. We present two options for assessment of 3D imaging quality, the use of microspheres functionalised for DNA-PAINT and a commercial DNA origami sample. A method to establish and assess a qPAINT workflow for quantitative imaging is demonstrated with a second, commercially available DNA origami sample.
Collapse
Affiliation(s)
- Ruisheng Lin
- Living Systems Institute and Biomedical Physics, University of Exeter, United Kingdom
| | - Alexander H Clowsley
- Living Systems Institute and Biomedical Physics, University of Exeter, United Kingdom
| | - Tobias Lutz
- Living Systems Institute and Biomedical Physics, University of Exeter, United Kingdom
| | - David Baddeley
- Department of Cell Biology, Yale University, USA; Bioengineering Institute, University of Auckland, New Zealand
| | - Christian Soeller
- Living Systems Institute and Biomedical Physics, University of Exeter, United Kingdom.
| |
Collapse
|
46
|
Yan T, Richardson CJ, Zhang M, Gahlmann A. Computational correction of spatially variant optical aberrations in 3D single-molecule localization microscopy. OPTICS EXPRESS 2019; 27:12582-12599. [PMID: 31052798 DOI: 10.1364/oe.27.012582] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/03/2019] [Indexed: 05/20/2023]
Abstract
3D single-molecule localization microscopy relies on fitting the shape of point-spread-functions (PSFs) recorded on a wide-field detector. However, optical aberrations distort those shapes, which compromises the accuracy and precision of single-molecule localization microscopy. Here, we employ a computational phase retrieval based on a vectorial PSF model to quantify the spatial variance of optical aberrations in a two-channel ultrawide-field single-molecule localization microscope. The use of a spatially variant PSF model enables accurate and precise emitter localization in x-, y- and z-directions throughout the entire field of view.
Collapse
|
47
|
Post RAJ, van der Zwaag D, Bet G, Wijnands SPW, Albertazzi L, Meijer EW, van der Hofstad RW. A stochastic view on surface inhomogeneity of nanoparticles. Nat Commun 2019; 10:1663. [PMID: 30971686 PMCID: PMC6458121 DOI: 10.1038/s41467-019-09595-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 03/19/2019] [Indexed: 01/16/2023] Open
Abstract
The interactions between and with nanostructures can only be fully understood when the functional group distribution on their surfaces can be quantified accurately. Here we apply a combination of direct stochastic optical reconstruction microscopy (dSTORM) imaging and probabilistic modelling to analyse molecular distributions on spherical nanoparticles. The properties of individual fluorophores are assessed and incorporated into a model for the dSTORM imaging process. Using this tailored model, overcounting artefacts are greatly reduced and the locations of dye labels can be accurately estimated, revealing their spatial distribution. We show that standard chemical protocols for dye attachment lead to inhomogeneous functionalization in the case of ubiquitous polystyrene nanoparticles. Moreover, we demonstrate that stochastic fluctuations result in large variability of the local group density between particles. These results cast doubt on the uniform surface coverage commonly assumed in the creation of amorphous functional nanoparticles and expose a striking difference between the average population and individual nanoparticle coverage. Determining the spatial arrangement of molecules on a nanoparticle’s surface is key to understanding its interactions. Here, the authors use dSTORM imaging and probabilistic modelling to map the distribution of fluorophores on a nanoparticle, finding that ligand coverage is heterogeneous and highly variable between individual particles.
Collapse
Affiliation(s)
- R A J Post
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Mathematics and Computer Science, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - D van der Zwaag
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,DSM Coating Resins, P.O. Box 123, 5145 PE, Waalwijk, The Netherlands
| | - G Bet
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Mathematics and Computer Science, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Mathematics and Computer Science 'Ulisse Dini', University of Florence, 50134, Florence, Italy
| | - S P W Wijnands
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - L Albertazzi
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - E W Meijer
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands. .,Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands. .,Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.
| | - R W van der Hofstad
- Institute of Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands. .,Department of Mathematics and Computer Science, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.
| |
Collapse
|
48
|
Cohen EAK, Abraham AV, Ramakrishnan S, Ober RJ. Resolution limit of image analysis algorithms. Nat Commun 2019; 10:793. [PMID: 30770826 PMCID: PMC6377644 DOI: 10.1038/s41467-019-08689-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 01/09/2019] [Indexed: 11/17/2022] Open
Abstract
The resolution of an imaging system is a key property that, despite many advances in optical imaging methods, remains difficult to define and apply. Rayleigh’s and Abbe’s resolution criteria were developed for observations with the human eye. However, modern imaging data is typically acquired on highly sensitive cameras and often requires complex image processing algorithms to analyze. Currently, no approaches are available for evaluating the resolving capability of such image processing algorithms that are now central to the analysis of imaging data, particularly location-based imaging data. Using methods of spatial statistics, we develop a novel algorithmic resolution limit to evaluate the resolving capabilities of location-based image processing algorithms. We show how insufficient algorithmic resolution can impact the outcome of location-based image analysis and present an approach to account for algorithmic resolution in the analysis of spatial location patterns. The resolution limitations when using the ubiquitous algorithms that process images obtained using modern techniques are not straightforward to define. Here, the authors examine the performance of localization algorithms and use spatial statistics to provide a metric for assessing the resolution limit of such algorithms.
Collapse
Affiliation(s)
- Edward A K Cohen
- Department of Mathematics, Imperial College London, London, SW7 2AZ, UK.
| | - Anish V Abraham
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA.,Department of Molecular & Cellular Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Sreevidhya Ramakrishnan
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA.,Department of Molecular & Cellular Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Raimund J Ober
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA. .,Department of Molecular & Cellular Medicine, Texas A&M University, College Station, TX, 77843, USA. .,Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.
| |
Collapse
|
49
|
TCR microclusters form spatially segregated domains and sequentially assemble in calcium-dependent kinetic steps. Nat Commun 2019; 10:277. [PMID: 30655520 PMCID: PMC6336795 DOI: 10.1038/s41467-018-08064-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 12/08/2018] [Indexed: 01/21/2023] Open
Abstract
Engagement of the T cell receptor (TCR) by stimulatory ligand results in the rapid formation of microclusters at sites of T cell activation. Whereas microclusters have been studied extensively using confocal microscopy, the spatial and kinetic relationships of their signaling components have not been well characterized due to limits in image resolution and acquisition speed. Here we show, using TIRF-SIM to examine the organization of microclusters at sub-diffraction resolution, the presence of two spatially distinct domains composed of ZAP70-bound TCR and LAT-associated signaling complex. Kinetic analysis of microcluster assembly reveal surprising delays between the stepwise recruitment of ZAP70 and signaling proteins to the TCR, as well as distinct patterns in their disassociation. These delays are regulated by intracellular calcium flux downstream of T cell activation. Our results reveal novel insights into the spatial and kinetic regulation of TCR microcluster formation and T cell activation. Engagement of T cell receptors (TCRs) induces the formation of microclusters that mediate the downstream signalling events. Here the authors show, using high resolution TIRF-SIM and live cell imaging, that ZAP70 and LAT are recruited to TCR with distinct kinetics, with the delayed ZAP70-TCR association modulated by TCR-induced calcium flux.
Collapse
|
50
|
Paul MW, de Gruiter HM, Lin Z, Baarends WM, van Cappellen WA, Houtsmuller AB, Slotman JA. SMoLR: visualization and analysis of single-molecule localization microscopy data in R. BMC Bioinformatics 2019; 20:30. [PMID: 30646838 PMCID: PMC6334411 DOI: 10.1186/s12859-018-2578-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/11/2018] [Indexed: 02/05/2023] Open
Abstract
Background Single-molecule localization microscopy is a super-resolution microscopy technique that allows for nanoscale determination of the localization and organization of proteins in biological samples. For biological interpretation of the data it is essential to extract quantitative information from the super-resolution data sets. Due to the complexity and size of these data sets flexible and user-friendly software is required. Results We developed SMoLR (Single Molecule Localization in R): a flexible framework that enables exploration and analysis of single-molecule localization data within the R programming environment. SMoLR is a package aimed at extracting, visualizing and analyzing quantitative information from localization data obtained by single-molecule microscopy. SMoLR is a platform not only to visualize nanoscale subcellular structures but additionally provides means to obtain statistical information about the distribution and localization of molecules within them. This can be done for individual images or SMoLR can be used to analyze a large set of super-resolution images at once. Additionally, we describe a method using SMoLR for image feature-based particle averaging, resulting in identification of common features among nanoscale structures. Conclusions Embedded in the extensive R programming environment, SMoLR allows scientists to study the nanoscale organization of biomolecules in cells by extracting and visualizing quantitative information and hence provides insight in a wide-variety of different biological processes at the single-molecule level. Electronic supplementary material The online version of this article (10.1186/s12859-018-2578-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Maarten W Paul
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - H Martijn de Gruiter
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Zhanmin Lin
- Department of Neuroscience, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Wiggert A van Cappellen
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands. .,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - Johan A Slotman
- Erasmus Optical Imaging Centre, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| |
Collapse
|